Molecular epidemiology of imipenem resistance in invasive Haemophilus influenzae infections in Germany in 2016

Amino acid substitutions in PBP3 in Haemophilus influenzae strains, their phenotypic detection and impact on resistance to β-lactams

BACKGROUND

Data from surveillance on antibiotic resistance have shown an increasing prevalence of non-enzymatic resistance (β-lactamase-negative ampicillin-resistant) to β-lactam antibiotics among H. influenzae strains in the Czech Republic. Aminopenicillins are recommended agents for non-invasive Haemophilus influenzae infections. The phenomenon of non-enzymatic resistance to β-lactams is complicated by the fact that the phenotypic detection of PBP3 with specific amino acid substitutions (rPBP3) is challenging, since rPBP3 isolates have repeatedly been demonstrated to be split by the epidemiological cut-off values (ECOFF) for aminopenicillins defined by EUCAST.

OBJECTIVES

We sought to determine whether the penicillin disc has sufficient detection ability to predict the non-enzymatic mechanism; whether other antibiotics can be used for detection; and what is the agreement between the broth microdilution and disc diffusion methods.

METHODS

We undertook susceptibility testing of selected antibiotics according to EUCAST of 153 rPBP3 strains, and sequencing of the ftsI gene to determination amino acid substitutions.

RESULTS

For a selected set of rPBP strains: (i) the detection capability for penicillin, ampicillin, cefuroxime and amoxicillin/clavulanate was found to be 91.5%, 94.4%, 89.5% and 70.6%, respectively; (ii) the categorical agreement between the disc diffusion method and the MIC for ampicillin and cefuroxime was 71.1% and 83.8%, respectively.

CONCLUSIONS

We observed better recognition of rPBP3 strains by the ampicillin disc than by the penicillin disc. There is frequently a discrepancy in the interpretation of susceptibility results between the methods used.

Antibiotic resistance and molecular characterization of non-invasive clinical Haemophilus influenzae isolates in Germany 2019 and 2020

Background

Haemophilus influenzae (Hi) is known as a cause of invasive and non-invasive diseases. Especially ear, nose and throat (ENT) infections are common reasons for antibiotic prescriptions in outpatient settings in Germany. Therefore, antibiotic resistance surveillance is important to provide the basis of recommendations for the empirical usage of antibiotic agents.

Objectives

To provide data on susceptibility rates of oral antibiotics for non-invasive clinical Hi isolates in Germany and to investigate molecular resistance patterns of β-lactams, ciprofloxacin, doxycycline and trimethoprim/sulfamethoxazole.

Methods

Isolates were collected from a sentinel network of diagnostic laboratories in a prospective multicentre prevalence study. Antibiotic susceptibility testing was done with a commercial broth microdilution kit. MICs were interpreted according to EUCAST guidelines. Resistance gene sequencing and WGS were performed to analyze molecular antibiotic resistance patterns and genetic relationships between the isolates.

Results

In total, 215 Hi isolates were collected from 23 laboratories across Germany. The highest resistance rates were found for amoxicillin (n = 30; 14%), cefuroxime (n = 40; 18.6%) and trimethoprim/sulfamethoxazole (co-trimoxazole) (n = 34; 15.8%). Resistance to amoxicillin was mainly due to blaTEM-1 (n = 29; 96.7%). PBP3 alterations were found in 39 of 40 cefuroxime-resistant isolates (97.5%). Two of the cefuroxime-resistant isolates harboured PBP3 mutation patterns that have not yet been associated with cefuroxime resistance; in one of them, a known lpoA mutation was found. One isolate showed no mutations in PBP3 or lpoA. All co-trimoxazole-resistant isolates (15.8%) showed known mutations in folA and its promoter region. Additionally, point mutations in folP were identified in a subset of these isolates. The most frequent sequence types (STs) were ST57 (n = 10) and ST103 (n = 10). Genetic cluster analysis identified six clusters, but no epidemiological link could be confirmed.

Conclusion

Resistance to oral antibiotics in non-invasive clinical Hi isolates in Germany was generally low. Amoxicillin is estimated to cover 86% of infections involving non-invasive Hi and, therefore, is still effective for the first-line empirical treatment for ENT infections in Germany. Further surveillance of antimicrobial susceptibility in non-invasive Hi isolates is important to ensure the data basis for guidelines of antibiotic usage.

Evolution of mutations in the ftsI gene leading to amino acid substitutions in PBP3 in Haemophilus influenzae strains under the selective pressure of ampicillin and cefuroxime

BACKGROUND

Aminopenicillins are recommended agents for non-invasive Haemophilus influenzae infections. One of the mechanisms of resistance to β-lactams is the alteration of the transpeptidase region of penicillin binding protein 3 (PBP3) which is caused by mutations in the ftsI gene. It was shown that exposure to beta-lactams has a stimulating effect on increase of prevalence of H. influenzae strains with the non-enzymatic mechanism of resistance.

OBJECTIVES

The aim of our study was to compare the mutational potential of ampicillin and cefuroxime in H. influenzae strains, determination of minimum inhibitory concentration and the evolution of mutations over time, focusing on amino acid substitutions in PBP3.

METHODS

30 days of serial passaging of strains in liquid broth containing increasing concentrations of ampicillin or cefuroxime was followed by whole-genome sequencing.

RESULTS

On average, cefuroxime increased the minimum inhibitory concentration more than ampicillin. The minimum inhibitory concentration was increased by a maximum of 32 fold. Substitutions in the PBP3 started to appear after 15 days of passaging. In PBP3, cefuroxime caused different substitutions than ampicillin.

CONCLUSIONS

Our experiment observed differences in mutation selection by ampicillin and cefuroxime. Selection pressure of antibiotics in vitro generated substitutions that do not occur in clinical strains in the Czech Republic.

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

Introduction

Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018-2019 by the Belgian National Reference Centre (NRC) for Haemophilus influenzae, as they presented an unusual multi-resistant profile.

Methods

All three isolates were sequenced by WGS and mapped to the reference isolate Hi Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in ftsI, murE and murF genes, and inner partial sequences were compared against the blast nucleotide database to look for similarity with other Haemophilus species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology.

Results

The isolates also harboured interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodelling events in ompP2 that might be related to lower carbapenem susceptibility.

Conclusion

The Hi evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family Pasteurellaceae. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping Hi AMR, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.

Imipenem heteroresistance but not tolerance in Haemophilus influenzae during chronic lung infection associated with chronic obstructive pulmonary disease

Antibiotic resistance is a major Public Health challenge worldwide. Mechanisms other than resistance are described as contributors to therapeutic failure. These include heteroresistance and tolerance, which escape the standardized procedures used for antibiotic treatment decision-making as they do not involve changes in minimal inhibitory concentration (MIC). Haemophilus influenzae causes chronic respiratory infection and is associated with exacerbations suffered by chronic obstructive pulmonary disease (COPD) patients. Although resistance to imipenem is rare in this bacterial species, heteroresistance has been reported, and antibiotic tolerance cannot be excluded. Moreover, development of antibiotic heteroresistance or tolerance during within-host H. influenzae pathoadaptive evolution is currently unknown. In this study, we assessed imipenem resistance, heteroresistance and tolerance in a previously sequenced longitudinal collection of H. influenzae COPD respiratory isolates. The use of Etest, disc diffusion, population analysis profiling, tolerance disc (TD)-test methods, and susceptibility breakpoint criteria when available, showed a significant proportion of imipenem heteroresistance with differences in terms of degree among strains, absence of imipenem tolerance, and no specific trends among serial and clonally related strains could be established. Analysis of allelic variation in the ftsI, acrA, acrB, and acrR genes rendered a panel of polymorphisms only found in heteroresistant strains, but gene expression and genome-wide analyses did not show clear genetic traits linked to heteroresistance. In summary, a significant proportion of imipenem heteroresistance was observed among H. influenzae strains isolated from COPD respiratory samples over time. These data should be useful for making more accurate clinical recommendations to COPD patients.

Antimicrobial Susceptibility Survey of Invasive Haemophilus influenzae in the United States in 2016

Antibiotics are important for the treatment and prevention of invasive Haemophilus influenzae disease. Reduced susceptibility to clinically relevant drugs, except ampicillin, has been uncommon in the United States. Susceptibility of 700 invasive H. influenzae isolates, collected through population-based surveillance during 2016, was assessed for 15 antibiotics using broth microdilution, according to the CLSI guidelines; a subset of 104 isolates were also assessed for rifampin susceptibility using Etest. Genomes were sequenced to identify genes and mutations known to be associated with reduced susceptibility to clinically relevant drugs. A total of 508 (72.6%) had reduced susceptibility to at least one antibiotic and more than half of the isolates exhibited reduced susceptibility to only one (33.6%) or two (21.6%) antibiotic classes. All tested isolates were susceptible to rifampin, a chemoprophylaxis agent, and <1% (n = 3) of isolates had reduced susceptibility to third generation cephalosporins, which are recommended for invasive disease treatment. In contrast, ampicillin resistance was more common (28.1%) and predominantly associated with the detection of a β-lactamase gene; 26.2% of isolates in the collection contained either a TEM-1 or ROB-1 β-lactamase gene, including 88.8% of ampicillin-resistant isolates. β-lactamase negative ampicillin-resistant (BLNAR) isolates were less common and associated with ftsI mutations; resistance to amoxicillin-clavulanate was detected in <2% (n = 13) of isolates. The proportion of reduced susceptibility observed was higher among nontypeable H. influenzae and serotype e than other serotypes. US invasive H. influenzae isolates remain predominantly susceptible to clinically relevant antibiotics except ampicillin, and BLNAR isolates remain uncommon. IMPORTANCE Antibiotics play an important role for the treatment and prevention of invasive Haemophilus influenzae disease. Antimicrobial resistance survey of invasive H. influenzae isolates collected in 2016 showed that the US H. influenzae population remained susceptible to clinically relevant antibiotics, except for ampicillin. Detection of approximately a quarter ampicillin-resistant and β-lactamase containing strains demonstrates that resistance mechanisms can be acquired and sustained within the H. influenzae population, highlighting the continued importance of antimicrobial resistance surveillance for H. influenzae to monitor susceptibility trends and mechanisms of resistance.

Invasive Haemophilus influenzae Infections after 3 Decades of Hib Protein Conjugate Vaccine Use

Haemophilus influenzae serotype b (Hib) was previously the most common cause of bacterial meningitis and an important etiologic agent of pneumonia in children aged <5 years. Its major virulence factor is the polyribosyl ribitol phosphate (PRP) polysaccharide capsule. In the 1980s, PRP-protein conjugate Hib vaccines were developed and are now included in almost all national immunization programs, achieving a sustained decline in invasive Hib infections. However, invasive Hib disease has not yet been eliminated in countries with low vaccine coverage, and sporadic outbreaks of Hib infection still occur occasionally in countries with high vaccine coverage. Over the past 2 decades, other capsulated serotypes have been recognized increasingly as causing invasive infections. H. influenzae serotype a (Hia) is now a major cause of invasive infection in Indigenous communities of North America, prompting a possible requirement for an Hia conjugate vaccine. H. influenzae serotypes e and f are now more common than serotype b in Europe. Significant year-to-year increases in nontypeable H. influenzae invasive infections have occurred in many regions of the world. Invasive H. influenzae infections are now seen predominantly in patients at the extremes of life and those with underlying comorbidities. This review provides a comprehensive and critical overview of the current global epidemiology of invasive H. influenzae infections in different geographic regions of the world. It discusses those now at risk of invasive Hib disease, describes the emergence of other severe invasive H. influenzae infections, and emphasizes the importance of long-term, comprehensive, clinical and microbiologic surveillance to monitor a vaccine's impact.

Characteristics and Antibiotic Resistance of Haemophilus influenzae in Children with Lower Respiratory Tract Infection in Chengdu, China

Background: Haemophilus influenzae is an opportunistic pathogen of the human respiratory tract. Haemophilus influenzae can cause not only respiratory tract infection in children but also otitis media, epiglottitis and sinusitis. With the widespread use of antibiotics, the positive rate of β-lactamase in H. influenzae is increasing, and the rate of antimicrobial resistance is also increasing, which increases the difficulty of clinical treatment. Objectives: To study the infection characteristics of patients and the antibiotic resistance of H. influenzae in lower respiratory tract samples of children in Chengdu, so as to provide a reference for its clinical diagnosis and the rational use of antibiotics. Methods: Sputum samples of 15891 children aged 0-14 years with lower respiratory tract infection were collected. Haemophilus influenzae was cultured and identified, its drug susceptibility tested, and the results determined according to the guidelines of CLSI 2020. Results: A total of 15891 clinical isolate strains in sputum were detected for drug sensitivity from December 2018 to January 2020, of which 5488 were H. influenzae, accounting for 34.54% (5488/15891). The sex of children infected with H. influenzae was not skewed (P > 0.05). The detection rate of H. influenzae was the highest in children aged 7 - 11 months, and the lowest was in the age group ≤ 28 d. The detection rate was the highest in spring and the lowest in autumn. The positive rate of β-lactamase was 92.0%, the resistance rate to ampicillin was 92.0%, the sensitivity to amoxicillin/clavulanate was 70.2%, and the sensitivity to cefotaxime, ofloxacin, tetracycline, chloramphenicol, and rifampicin was more than 90.0%. Conclusions: Children aged 7 months to 14 years were generally susceptible to H. influenzae in spring, and the positive rate of β-lactamase was high. Doctors should refer to the infection characteristics and drug resistance of H. influenzae and choose antibiotics correctly to better control the infection.